- galaxy-dev - lists.galaxyproject.org

fastq_combiner
by Jennifer Hillman-Jackson 07 Jan '13

07 Jan '13

Hello, The tool you are looking for is: galaxy-dist / tools / fastq / fastq_combiner.py galaxy-dist / tools / fastq / fastq_combiner.xml Hopefully this helps. Next time, please be sure to send questions directly to the galaxy-dev(a)bx.psu.edu email address. Your question went to "galaxy-dev-owner(a)lists.bx.psu.edu" originally, which is not the mailing list, but a way to reach the list moderators if there is a technical problem. Take care, Jen Galaxy team On 1/7/13 3:09 AM, wei liu wrote:> Dear all, > > I have used the local galaxy, and I want to find out which script is > used to Combine FASTA and QUAL > <https://main.g2.bx.psu.edu/tool_runner?tool_id=fastq_combiner> into > FASTQ. I have tried the scripts in > galaxy-dist/tools/next_gen_conversion/solid2fastq.py, but it can not > merge the several lines which belong to the same sequence. > > Looking forward for your reply! > > Best Regards, > Wei Liu. -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Re: [galaxy-dev] Galaxy cloud: Tool execution generated the following error message
by Brad Chapman 07 Jan '13

07 Jan '13

Alicia; Thanks for the useful feedback. I'm agreed that Cloud Galaxy usage requires more IT knowledge compared to running directly on a hosted Galaxy instance. Dannon, Enis and everyone are working hard to make it easier, but at this point it does require understanding Amazon EC2. For your termination problem, you want to be sure to quit using the CloudMan web admin interface. In the terminate dialog, there is a checkbox you can click to delete all of the EBS volumes associated with a cluster. This is off by default to avoid deleting important data, but if you check it this should remove all of your associated data files. For the AMI issue, I have to defer back to Dannon as I'm not sure how they're handling the markupsafe egg conflict with the official AMI. Dannon, happy to coordinate on the new CloudBioLinux if that helps at all. Thanks again for the helpful feedback, Brad > Thank you for your message. > > I followed the instructions on "http://wiki.galaxyproject.org/CloudMan". I > created an Amazon account, and also ollowed a tutorial video in setting up > the account. The wiki page recommended the AMI as below: > > *Current AMI:* > > - AMI: ami-da58aab3 > - Name: 861460482541/galaxy-cloudman-2011-03-22 > > By the way, I find it quite confusing to use the Amazon Web services > (probably due to the fact that I'm not a computer scientist, just a > research assistant trying to analyse her data). All the different > charges/storage quite are confusing. I'm now being charged for USD10 for a > Elastic block storage even though I have deleted all the instances. There > is also no way to contact Amazon tech support as you need to pay a > subscription fee first. This is very different from Penguin COmputing who > works with Life Tech. We are Ion Torrent users, and sometimes use the cloud > services, the support at Penguin Comp are very responsive, and there is no > hidden costs like the EBS, which are tucked away at another corner, > charging me for the storage even though I've deleted the instances. Luckily > I keep checking the account statement and managed to find the hidden EBS, > and quickly deleted all the volumes that i didn't even know I have created! > > I would prefer to use the public server as it seems so much, I think Galaxy > is really a very useful tool for non-bioinformaticians like me, and I do > not mind having to pay a subscription fee use the public server if funding > is a issue. Recently the web-based platform seems to be quite unstable, it > hangs or the page just could not be loaded (DNS missing..) That's why i > went to use the Galaxy cloud, but it didnt work. > > Best regards > Alicia > > > On Fri, Jan 4, 2013 at 9:53 PM, Brad Chapman <chapmanb(a)50mail.com> wrote: > >> >> Alicia; >> >> > *I hope this is the correct email to contact re. Galaxy cloud. I tried to >> > run Galaxy on the cloud, I could upload the file but could not go beyond >> > simple function "operate on genomic intervals". Is this normal? This is >> my >> > first time using the Galaxy on the cloud. Hope to hear from you soon. >> Thank >> > you. * >> [...] >> > /mnt/galaxyTools/galaxy-central/lib/galaxy/__init__.py:79: >> > UserWarning: Module markupsafe was already imported from >> > >> /usr/local/lib/python2.6/dist-packages/MarkupSafe-0.11-py2.6-linux-x86_64.egg/markupsafe/__init__.pyc, >> > but >> /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg >> > is being added to sys.path >> >> What method did you use to start up the Galaxy cloud instance? I've seen >> this problem with recent versions of Galaxy and BioCloudCentral, using >> the current CloudBioLinux AMI (ami-46d4792f). We have a new version of >> CloudBioLinux/CloudMan in development which fixes this. In the short >> term, you could try the Galaxy Cloud Launch page to create your instance: >> >> https://main.g2.bx.psu.edu/cloudlaunch >> >> Dannon and Enis, we could isolate Galaxy inside a virtualenv as a more >> general fix to these egg conflicts. >> >> Hope this helps, >> Brad >>

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Custom Builds Error Message
by Claire Ellis 05 Jan '13

05 Jan '13

Hello, I am having a problem accessing the "custom builds" toolset. I am getting an error message when I click on custom builds, and this has been happening for few weeks now. Any advice you can give would be greatly appreciated. Thanks

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updates with hg incoming
by julie dubois 04 Jan '13

04 Jan '13

Hi all, I wondered if when we make an update via hh it erased the previous files or if that added the modifications to files. Because I've modified several scripts to customize my local galaxy and I don't want that these modifications desappear with an update. Thanks. julie

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Galaxy cloud: Tool execution generated the following error message
by Poh Leng Chong 04 Jan '13

04 Jan '13

*Hi * *Happy New Year!* *I hope this is the correct email to contact re. Galaxy cloud. I tried to run Galaxy on the cloud, I could upload the file but could not go beyond simple function "operate on genomic intervals". Is this normal? This is my first time using the Galaxy on the cloud. Hope to hear from you soon. Thank you. * *Best wishes* *alicia* *Dataset 7: Join on data 1 and data 5* Tool execution generated the following error message: /mnt/galaxyTools/galaxy-central/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/local/lib/python2.6/dist-packages/MarkupSafe-0.11-py2.6-linux-x86_64.egg/markupsafe/__init__.pyc, but /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() Dataset generation errors *Dataset 8: Intersect on data 1 and data 5* Tool execution generated the following error message: /mnt/galaxyTools/galaxy-central/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/local/lib/python2.6/dist-packages/MarkupSafe-0.11-py2.6-linux-x86_64.egg/markupsafe/__init__.pyc, but /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict()

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hg pull aborted
by Sarah Maman 04 Jan '13

04 Jan '13

Hello, When updating local instance of our Galaxy, the hg aborted: pulling from https://bitbucket.org/galaxy/galaxy-dist/ searching for changes adding changesets adding manifests adding file changes added 1482 changesets with 3989 changes to 1340 files abort: untracked file in working directory differs from file in requested revision: 'doc/Makefile' and : -bash-3.2$ hg update abort: untracked file in working directory differs from file in requested revision: 'doc/source/conf.py' Could you please tell me what this may be the problem? Thanks

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Error trying to see the installed dependency in Galaxy for PICARD
by Anthonius deBoer 04 Jan '13

04 Jan '13

Hi, I installed PICARD from the main tool shed in the latest update from galaxy-dist and when I clicked on the picard installed dependency link in the admin tool, I got this... Error Traceback: View as: Interactive | Text | XML (full) ⇝ TypeError: 'NoneType' object is not iterable URL: http://srv151/admin_toolshed/browse_tool_dependency?repository_id=a799d3867… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:91 in __call__ view >> return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.framework:206 in decorator view >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:422 in browse_tool_dependency view >> tool_dependency.error_message = suc.to_safe_string( tool_dependency.error_message ) Module galaxy.util.shed_util_common:2138 in to_safe_string view >> for c in text: TypeError: 'NoneType' object is not iterable Extra Features >> Display the lines of code near each part of the traceback Show a debug prompt to allow you to directly debug the code at the traceback I also found I always have to restart GALAXY after I install something from the toolshed otherwise I get this: Tool 'toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.1.0' does not exist, kwd={} I have to restart galaxy (updating the metadata in the admin does not fix this..) Any ideas? Thon

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Getting error when trying to run CIRCSTER
by Anthonius deBoer 04 Jan '13

04 Jan '13

Got this when trying CIRCSTER on latest galaxy-dist. Does this mean my system does not know about certain genomes? Trackster works fine... Thon Error Traceback: View as: Interactive | Text | XML (full) ⇝ TypeError: argument of type 'NoneType' is not iterable URL: http://srv151/visualization/circster?dataset_id=241d84796a24640a&hda_ldda=h… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:91 in __call__ view >> return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.visualization:748 in circster view >> chroms_info = self.app.genomes.chroms( trans, dbkey=dbkey ) Module galaxy.visualization.genomes:210 in chroms view >> dbkey_owner, dbkey = decode_dbkey( dbkey ) Module galaxy.visualization.genomes:24 in decode_dbkey view >> if ':' in dbkey: TypeError: argument of type 'NoneType' is not iterable

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gatk lite
by mark.rose＠syngenta.com 04 Jan '13

04 Jan '13

Hello Is it possible to redirect the GATK tools in my local installation of Galaxy to use GATK Lite (which is free) rather than GATK. If so what files would need to be altered and how? I'm particularly interested in getting the "Depth of Coverage" tool to work. Thanks much Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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issue with galaxy server running samtools merge
by chodon sass 03 Jan '13

03 Jan '13

hi, i am trying to merge several bam files with samtools merge on the galaxy server. i did this a few days ago with the same files successfully but when i tried to run this merge on the same files again, i have had some strange behavior from galaxy server. first, the commands didn't start to run for several hours. seconde, they are taking a very long time - this morning they are still running! there are only 3 bams in each merge command and on my home computer this take seconds to minutes. i don't think there is anything wrong with the file format, as the command ran successfully a few days ago on the same files. could there be something going on on the galaxy server side? thanks! chodon

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